scPDB - 3l9m entry

Protein Data Bank Entry:

PDB ID : 3l9m

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2010-01-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	cAMP-dependent protein kinase catalytic subunit alpha
ID:	KAPCA_HUMAN
AC:	P17612
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.11.11

Chains:

Chain Name:	Percentage of Residues within binding site
B	94 %
D	6 %

Ligand binding site composition:

B-Factor:	16.562
Number of residues:	38
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.282	985.500

% Hydrophobic	% Polar
51.71	48.29
According to VolSite

Ligand :

HET Code:	L9M
Formula:	C20H23N6S
Molecular weight:	379.502 g/mol
DrugBank ID:	-
Buried Surface Area:	72.59 %
Polar Surface area:	122.36 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
74.6453	94.2251	25.7254

Binding mode :

What is Poseview ?

2D View
3D View

Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
C18	CD1	LEU- 49	4.14	0	Hydrophobic	false
CL1	CB	LEU- 49	4.32	0	Hydrophobic	false
C7	CD2	PHE- 54	3.38	0	Hydrophobic	false
S1	CG2	VAL- 57	3.76	0	Hydrophobic	false
C16	CG1	VAL- 57	4.01	0	Hydrophobic	false
C14	CB	ALA- 70	3.49	0	Hydrophobic	false
N2	NZ	LYS- 72	3.12	138.63	H-Bond (Protein Donor)	false
C13	CG1	VAL- 104	3.99	0	Hydrophobic	false
C13	SD	MET- 120	3.75	0	Hydrophobic	false
C11	CE	MET- 120	3.36	0	Hydrophobic	false
N4	O	GLU- 121	2.75	171.63	H-Bond (Ligand Donor)	false
C18	CE1	TYR- 122	4.36	0	Hydrophobic	false
N1	N	ALA- 123	3.21	158.26	H-Bond (Protein Donor)	false
C2	CG	GLU- 127	3.67	0	Hydrophobic	false
N3	OD1	ASN- 171	2.66	146.95	H-Bond (Ligand Donor)	false
C15	CG	MET- 173	4.3	0	Hydrophobic	false
C18	SD	MET- 173	4	0	Hydrophobic	false
C2	CE	MET- 173	3.44	0	Hydrophobic	false
C17	CB	THR- 183	3.7	0	Hydrophobic	false
C11	CG2	THR- 183	3.68	0	Hydrophobic	false
N3	OD2	ASP- 184	2.88	161.8	H-Bond (Ligand Donor)	false
N6	OD2	ASP- 184	2.87	125.88	H-Bond (Ligand Donor)	false
N3	OD2	ASP- 184	2.88	0	Ionic (Ligand Cationic)	false
C18	CE1	PHE- 327	3.53	0	Hydrophobic	false
CL1	CE1	PHE- 327	3.64	0	Hydrophobic	false
N5	O	HOH- 472	2.97	179.96	H-Bond (Protein Donor)	false